Multiple sequence alignment - TraesCS4D01G265600

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS4D01G265600 chr4D 100.000 3208 0 0 1 3208 435648735 435651942 0.000000e+00 5925.0
1 TraesCS4D01G265600 chr4B 93.968 2918 125 32 324 3208 536917428 536920327 0.000000e+00 4366.0
2 TraesCS4D01G265600 chr4B 93.773 819 24 7 2412 3208 537153681 537154494 0.000000e+00 1205.0
3 TraesCS4D01G265600 chr4B 82.773 238 25 6 1 233 536917216 536917442 7.020000e-47 198.0
4 TraesCS4D01G265600 chr4A 95.243 2060 79 11 336 2387 37030634 37032682 0.000000e+00 3243.0
5 TraesCS4D01G265600 chr4A 91.037 926 27 22 2311 3208 37032684 37033581 0.000000e+00 1199.0
6 TraesCS4D01G265600 chr4A 86.777 242 12 10 1 233 37030398 37030628 5.310000e-63 252.0
7 TraesCS4D01G265600 chr4A 94.000 100 5 1 229 328 64574119 64574021 1.990000e-32 150.0
8 TraesCS4D01G265600 chr4A 90.000 110 8 2 229 338 657204774 657204668 4.320000e-29 139.0
9 TraesCS4D01G265600 chr4A 89.286 112 9 3 229 340 420020471 420020363 1.550000e-28 137.0
10 TraesCS4D01G265600 chr7A 91.071 112 7 3 229 339 692343530 692343421 7.170000e-32 148.0
11 TraesCS4D01G265600 chr7A 90.654 107 8 2 229 335 731343408 731343304 1.200000e-29 141.0
12 TraesCS4D01G265600 chr3B 94.737 95 5 0 229 323 354006514 354006608 7.170000e-32 148.0
13 TraesCS4D01G265600 chr1D 89.076 119 10 3 229 346 277361232 277361116 9.280000e-31 145.0
14 TraesCS4D01G265600 chr1A 89.076 119 10 3 229 346 350015813 350015697 9.280000e-31 145.0
15 TraesCS4D01G265600 chr1A 89.815 108 11 0 229 336 550884939 550884832 4.320000e-29 139.0
16 TraesCS4D01G265600 chr2D 87.654 81 10 0 2010 2090 143757886 143757806 9.470000e-16 95.3
17 TraesCS4D01G265600 chr2B 87.654 81 10 0 2010 2090 201769433 201769353 9.470000e-16 95.3
18 TraesCS4D01G265600 chr2A 87.654 81 10 0 2010 2090 157547375 157547455 9.470000e-16 95.3


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4D01G265600 chr4D 435648735 435651942 3207 False 5925.000000 5925 100.0000 1 3208 1 chr4D.!!$F1 3207
1 TraesCS4D01G265600 chr4B 536917216 536920327 3111 False 2282.000000 4366 88.3705 1 3208 2 chr4B.!!$F2 3207
2 TraesCS4D01G265600 chr4B 537153681 537154494 813 False 1205.000000 1205 93.7730 2412 3208 1 chr4B.!!$F1 796
3 TraesCS4D01G265600 chr4A 37030398 37033581 3183 False 1564.666667 3243 91.0190 1 3208 3 chr4A.!!$F1 3207

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
271 284 0.106149 AGACACAAAGTGGTCGGACC 59.894 55.0 20.36 20.36 37.94 4.46 F
275 288 0.108019 ACAAAGTGGTCGGACCCTTC 59.892 55.0 23.81 13.97 37.50 3.46 F
276 289 0.605589 CAAAGTGGTCGGACCCTTCC 60.606 60.0 23.81 9.51 37.50 3.46 F
442 460 0.655733 GCGGTATGTGCTGCGTAAAT 59.344 50.0 0.00 0.00 0.00 1.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1708 1732 0.622136 ACCAGGCTCATCTGCATCAA 59.378 50.000 0.00 0.0 33.64 2.57 R
1924 1948 1.141881 GGCGCCTCAGAAGAATCGA 59.858 57.895 22.15 0.0 0.00 3.59 R
2195 2219 1.470494 GCAGCAACTTAGAAGAAGGCC 59.530 52.381 0.00 0.0 0.00 5.19 R
2242 2269 3.070018 CCTTAGTGAGGCAAACAGAGTG 58.930 50.000 0.00 0.0 39.09 3.51 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 61 2.294233 CCAAACCTCCATGTCTTGTGTG 59.706 50.000 0.00 0.00 0.00 3.82
61 62 2.951642 CAAACCTCCATGTCTTGTGTGT 59.048 45.455 0.00 0.00 0.00 3.72
64 65 2.092429 ACCTCCATGTCTTGTGTGTGTT 60.092 45.455 0.00 0.00 0.00 3.32
80 86 3.309954 GTGTGTTGGTTCTGTCTGTTCTC 59.690 47.826 0.00 0.00 0.00 2.87
91 97 2.290260 TGTCTGTTCTCGATTTGGGCAT 60.290 45.455 0.00 0.00 0.00 4.40
98 104 1.605710 CTCGATTTGGGCATGGATCAC 59.394 52.381 0.00 0.00 0.00 3.06
99 105 0.670162 CGATTTGGGCATGGATCACC 59.330 55.000 0.00 0.00 0.00 4.02
100 106 1.751733 CGATTTGGGCATGGATCACCT 60.752 52.381 0.00 0.00 37.04 4.00
101 107 1.959282 GATTTGGGCATGGATCACCTC 59.041 52.381 0.00 0.00 37.04 3.85
102 108 0.394216 TTTGGGCATGGATCACCTCG 60.394 55.000 0.00 0.00 37.04 4.63
103 109 1.561769 TTGGGCATGGATCACCTCGT 61.562 55.000 0.00 0.00 37.04 4.18
104 110 1.224592 GGGCATGGATCACCTCGTT 59.775 57.895 0.00 0.00 37.04 3.85
123 129 0.759959 TCCTCGTACTTGTTTGGGCA 59.240 50.000 0.00 0.00 0.00 5.36
129 135 2.549349 CGTACTTGTTTGGGCAGTAGGT 60.549 50.000 0.00 0.00 0.00 3.08
233 246 6.605849 GCTTGTGGCATTGATGTATATGTAG 58.394 40.000 0.00 0.00 41.35 2.74
235 248 5.559770 TGTGGCATTGATGTATATGTAGGG 58.440 41.667 0.00 0.00 0.00 3.53
238 251 5.009631 GGCATTGATGTATATGTAGGGCAA 58.990 41.667 0.00 0.00 0.00 4.52
239 252 5.124457 GGCATTGATGTATATGTAGGGCAAG 59.876 44.000 0.00 0.00 0.00 4.01
240 253 5.124457 GCATTGATGTATATGTAGGGCAAGG 59.876 44.000 0.00 0.00 0.00 3.61
241 254 4.286297 TGATGTATATGTAGGGCAAGGC 57.714 45.455 0.00 0.00 0.00 4.35
242 255 3.909995 TGATGTATATGTAGGGCAAGGCT 59.090 43.478 0.00 0.00 0.00 4.58
243 256 3.769739 TGTATATGTAGGGCAAGGCTG 57.230 47.619 0.00 0.00 0.00 4.85
254 267 2.332063 GCAAGGCTGCCTACAATAGA 57.668 50.000 23.69 0.00 43.26 1.98
255 268 1.943340 GCAAGGCTGCCTACAATAGAC 59.057 52.381 23.69 1.69 43.26 2.59
256 269 2.680805 GCAAGGCTGCCTACAATAGACA 60.681 50.000 23.69 0.00 43.26 3.41
257 270 2.939103 CAAGGCTGCCTACAATAGACAC 59.061 50.000 23.69 0.00 31.13 3.67
258 271 2.187958 AGGCTGCCTACAATAGACACA 58.812 47.619 21.98 0.00 28.47 3.72
259 272 2.571653 AGGCTGCCTACAATAGACACAA 59.428 45.455 21.98 0.00 28.47 3.33
260 273 3.009033 AGGCTGCCTACAATAGACACAAA 59.991 43.478 21.98 0.00 28.47 2.83
261 274 3.375299 GGCTGCCTACAATAGACACAAAG 59.625 47.826 12.43 0.00 0.00 2.77
262 275 4.003648 GCTGCCTACAATAGACACAAAGT 58.996 43.478 0.00 0.00 0.00 2.66
263 276 4.142816 GCTGCCTACAATAGACACAAAGTG 60.143 45.833 0.00 0.00 39.75 3.16
264 277 4.323417 TGCCTACAATAGACACAAAGTGG 58.677 43.478 1.93 0.00 37.94 4.00
265 278 4.202419 TGCCTACAATAGACACAAAGTGGT 60.202 41.667 1.93 0.00 37.94 4.16
266 279 4.392138 GCCTACAATAGACACAAAGTGGTC 59.608 45.833 1.93 0.00 37.94 4.02
267 280 4.625742 CCTACAATAGACACAAAGTGGTCG 59.374 45.833 1.93 0.00 37.94 4.79
268 281 3.399330 ACAATAGACACAAAGTGGTCGG 58.601 45.455 1.93 0.00 37.94 4.79
269 282 3.070446 ACAATAGACACAAAGTGGTCGGA 59.930 43.478 1.93 0.00 37.94 4.55
270 283 2.806608 TAGACACAAAGTGGTCGGAC 57.193 50.000 0.00 0.00 37.94 4.79
271 284 0.106149 AGACACAAAGTGGTCGGACC 59.894 55.000 20.36 20.36 37.94 4.46
272 285 0.883370 GACACAAAGTGGTCGGACCC 60.883 60.000 23.81 14.91 37.50 4.46
273 286 1.342672 ACACAAAGTGGTCGGACCCT 61.343 55.000 23.81 16.82 37.50 4.34
274 287 0.179029 CACAAAGTGGTCGGACCCTT 60.179 55.000 23.81 21.08 37.50 3.95
275 288 0.108019 ACAAAGTGGTCGGACCCTTC 59.892 55.000 23.81 13.97 37.50 3.46
276 289 0.605589 CAAAGTGGTCGGACCCTTCC 60.606 60.000 23.81 9.51 37.50 3.46
277 290 1.775934 AAAGTGGTCGGACCCTTCCC 61.776 60.000 23.81 7.17 38.99 3.97
278 291 3.714001 GTGGTCGGACCCTTCCCC 61.714 72.222 23.81 0.00 38.99 4.81
285 298 4.735599 GACCCTTCCCCGGACCCT 62.736 72.222 0.73 0.00 0.00 4.34
312 325 2.203070 GGAGCTACATGCACCCGG 60.203 66.667 0.00 0.00 45.00 5.73
313 326 2.897350 GAGCTACATGCACCCGGC 60.897 66.667 0.00 0.00 45.94 6.13
314 327 3.391665 GAGCTACATGCACCCGGCT 62.392 63.158 0.00 5.89 45.94 5.52
315 328 3.204827 GCTACATGCACCCGGCTG 61.205 66.667 0.00 0.00 45.15 4.85
316 329 3.204827 CTACATGCACCCGGCTGC 61.205 66.667 15.10 15.10 45.15 5.25
317 330 4.794648 TACATGCACCCGGCTGCC 62.795 66.667 18.95 9.11 45.15 4.85
327 340 0.682855 CCCGGCTGCCCTTTTATTGA 60.683 55.000 14.12 0.00 0.00 2.57
331 344 2.948979 CGGCTGCCCTTTTATTGATGTA 59.051 45.455 14.12 0.00 0.00 2.29
333 346 4.759693 CGGCTGCCCTTTTATTGATGTATA 59.240 41.667 14.12 0.00 0.00 1.47
363 376 4.393062 CGCCTGAATCTCAACATTTGTAGT 59.607 41.667 0.00 0.00 0.00 2.73
441 459 0.670854 TGCGGTATGTGCTGCGTAAA 60.671 50.000 0.00 0.00 43.32 2.01
442 460 0.655733 GCGGTATGTGCTGCGTAAAT 59.344 50.000 0.00 0.00 0.00 1.40
443 461 1.332904 GCGGTATGTGCTGCGTAAATC 60.333 52.381 0.00 0.00 0.00 2.17
444 462 1.930503 CGGTATGTGCTGCGTAAATCA 59.069 47.619 0.00 0.00 0.00 2.57
445 463 2.285602 CGGTATGTGCTGCGTAAATCAC 60.286 50.000 0.00 0.00 0.00 3.06
454 472 3.723835 GCTGCGTAAATCACCGTTTACAG 60.724 47.826 9.39 0.00 42.10 2.74
470 488 1.526686 CAGGCTGTGGTGAAGCACA 60.527 57.895 14.10 14.10 42.69 4.57
472 490 1.103398 AGGCTGTGGTGAAGCACAAC 61.103 55.000 15.45 11.35 42.69 3.32
492 512 2.093553 ACATTTGTGCTGGTTGTGCTTT 60.094 40.909 0.00 0.00 0.00 3.51
494 514 3.876274 TTTGTGCTGGTTGTGCTTTAA 57.124 38.095 0.00 0.00 0.00 1.52
495 515 4.399004 TTTGTGCTGGTTGTGCTTTAAT 57.601 36.364 0.00 0.00 0.00 1.40
496 516 5.521906 TTTGTGCTGGTTGTGCTTTAATA 57.478 34.783 0.00 0.00 0.00 0.98
497 517 4.764679 TGTGCTGGTTGTGCTTTAATAG 57.235 40.909 0.00 0.00 0.00 1.73
502 522 6.316390 GTGCTGGTTGTGCTTTAATAGTAGAT 59.684 38.462 0.00 0.00 0.00 1.98
562 584 7.054124 TCAAGTCTGAATTTGTGTTCCTAACT 58.946 34.615 0.00 0.00 0.00 2.24
585 607 2.568623 TTGGGTGCTCTTCTTCCTTC 57.431 50.000 0.00 0.00 0.00 3.46
586 608 1.434188 TGGGTGCTCTTCTTCCTTCA 58.566 50.000 0.00 0.00 0.00 3.02
588 610 2.174639 TGGGTGCTCTTCTTCCTTCAAA 59.825 45.455 0.00 0.00 0.00 2.69
589 611 2.816672 GGGTGCTCTTCTTCCTTCAAAG 59.183 50.000 0.00 0.00 0.00 2.77
590 612 3.496870 GGGTGCTCTTCTTCCTTCAAAGA 60.497 47.826 0.00 0.00 33.50 2.52
594 616 5.974158 GTGCTCTTCTTCCTTCAAAGAAAAC 59.026 40.000 1.26 0.00 42.93 2.43
595 617 5.067805 TGCTCTTCTTCCTTCAAAGAAAACC 59.932 40.000 1.26 0.00 42.93 3.27
598 620 4.536295 TCTTCCTTCAAAGAAAACCCCT 57.464 40.909 0.00 0.00 32.42 4.79
620 643 1.003718 GGTTTCCTCGGACCACCAG 60.004 63.158 8.14 0.00 35.95 4.00
805 828 9.232082 CAACATGATTAAATATGTTTACCACCG 57.768 33.333 14.48 3.17 43.00 4.94
877 900 1.621992 ATGTCACTGTCTCGTGTCCT 58.378 50.000 0.00 0.00 36.33 3.85
996 1019 6.007076 TGTTAATTGCAGTCTTGGAATACCA 58.993 36.000 0.00 0.00 43.53 3.25
1188 1211 1.890876 AGCAGGACGTGTATGCAAAA 58.109 45.000 15.98 0.00 42.45 2.44
1491 1514 0.685097 TGCACCTGTCCCTGTCTTAC 59.315 55.000 0.00 0.00 0.00 2.34
1670 1693 4.392921 AGTATTTCGAGATGGACTGTGG 57.607 45.455 0.00 0.00 0.00 4.17
1790 1814 1.825281 GCCCTGTGAGCTGTGTCTCT 61.825 60.000 0.00 0.00 34.29 3.10
1924 1948 0.743097 GTTACTACGGATGGCGAGGT 59.257 55.000 0.00 0.00 0.00 3.85
2100 2124 1.215382 CCGCTGGATGTCGAGAACA 59.785 57.895 0.00 0.00 43.51 3.18
2121 2145 1.001597 GTAGTCCCTCGGCTGATAACG 60.002 57.143 0.00 0.00 0.00 3.18
2147 2171 2.229062 CTCGAGTACAACAGAGAAGCCA 59.771 50.000 3.62 0.00 32.84 4.75
2195 2219 2.122768 AGGGTCTTCTATGGAAGCAGG 58.877 52.381 13.67 0.00 46.12 4.85
2242 2269 0.755686 AGCTAGGCTGGCTCATACAC 59.244 55.000 20.63 0.00 37.57 2.90
2309 2336 8.154649 ACTTGTATTGCTAATAGTGTTATGCC 57.845 34.615 0.00 0.00 0.00 4.40
2387 2415 7.608153 TGTGTAACATAGTGTACTACTGCATT 58.392 34.615 7.85 0.00 45.67 3.56
2438 2524 3.486383 TGAGTTGCCTGGAGTTTTTAGG 58.514 45.455 0.00 0.00 34.67 2.69
2442 2528 1.146982 TGCCTGGAGTTTTTAGGGCTT 59.853 47.619 0.00 0.00 40.15 4.35
2502 2592 4.569943 TCAGCTAACACATCAGGAAACTC 58.430 43.478 0.00 0.00 40.21 3.01
2520 2612 7.611467 AGGAAACTCTGTCATTTGCACAATATA 59.389 33.333 0.00 0.00 32.90 0.86
2521 2613 8.408601 GGAAACTCTGTCATTTGCACAATATAT 58.591 33.333 0.00 0.00 0.00 0.86
2532 2624 9.661187 CATTTGCACAATATATTCTCTTGAGTC 57.339 33.333 0.00 0.00 0.00 3.36
2537 2629 6.476706 CACAATATATTCTCTTGAGTCGCACA 59.523 38.462 0.00 0.00 0.00 4.57
2606 2704 3.610040 AACTCGACCACTGCATAATCA 57.390 42.857 0.00 0.00 0.00 2.57
2837 2939 9.753674 AAAGTTTACATGATTCAAATCTCCCTA 57.246 29.630 0.00 0.00 36.39 3.53
2961 3080 2.161486 CCTTTCTCGGCGCTTCTCG 61.161 63.158 7.64 1.53 42.12 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 61 2.540101 CGAGAACAGACAGAACCAACAC 59.460 50.000 0.00 0.00 0.00 3.32
61 62 2.429250 TCGAGAACAGACAGAACCAACA 59.571 45.455 0.00 0.00 0.00 3.33
64 65 4.058124 CAAATCGAGAACAGACAGAACCA 58.942 43.478 0.00 0.00 0.00 3.67
80 86 0.670162 GGTGATCCATGCCCAAATCG 59.330 55.000 0.00 0.00 0.00 3.34
91 97 0.611062 ACGAGGAACGAGGTGATCCA 60.611 55.000 0.00 0.00 41.86 3.41
98 104 2.719426 AACAAGTACGAGGAACGAGG 57.281 50.000 0.00 0.00 45.77 4.63
99 105 2.729882 CCAAACAAGTACGAGGAACGAG 59.270 50.000 0.00 0.00 45.77 4.18
100 106 2.546373 CCCAAACAAGTACGAGGAACGA 60.546 50.000 0.00 0.00 45.77 3.85
102 108 1.534163 GCCCAAACAAGTACGAGGAAC 59.466 52.381 0.00 0.00 0.00 3.62
103 109 1.141254 TGCCCAAACAAGTACGAGGAA 59.859 47.619 0.00 0.00 0.00 3.36
104 110 0.759959 TGCCCAAACAAGTACGAGGA 59.240 50.000 0.00 0.00 0.00 3.71
135 141 0.557729 CCAATAACCCCATCCCTGCT 59.442 55.000 0.00 0.00 0.00 4.24
136 142 0.261696 ACCAATAACCCCATCCCTGC 59.738 55.000 0.00 0.00 0.00 4.85
142 150 4.825085 CGTAAATAGCACCAATAACCCCAT 59.175 41.667 0.00 0.00 0.00 4.00
222 235 3.560025 GCAGCCTTGCCCTACATATACAT 60.560 47.826 0.00 0.00 44.74 2.29
238 251 2.187958 TGTGTCTATTGTAGGCAGCCT 58.812 47.619 20.63 20.63 41.77 4.58
239 252 2.691409 TGTGTCTATTGTAGGCAGCC 57.309 50.000 1.84 1.84 41.77 4.85
240 253 4.003648 ACTTTGTGTCTATTGTAGGCAGC 58.996 43.478 0.00 0.00 41.77 5.25
241 254 4.393062 CCACTTTGTGTCTATTGTAGGCAG 59.607 45.833 0.00 0.00 41.77 4.85
242 255 4.202419 ACCACTTTGTGTCTATTGTAGGCA 60.202 41.667 0.00 0.00 38.24 4.75
243 256 4.324267 ACCACTTTGTGTCTATTGTAGGC 58.676 43.478 0.00 0.00 0.00 3.93
244 257 4.625742 CGACCACTTTGTGTCTATTGTAGG 59.374 45.833 0.00 0.00 0.00 3.18
245 258 4.625742 CCGACCACTTTGTGTCTATTGTAG 59.374 45.833 0.00 0.00 0.00 2.74
246 259 4.281435 TCCGACCACTTTGTGTCTATTGTA 59.719 41.667 0.00 0.00 0.00 2.41
247 260 3.070446 TCCGACCACTTTGTGTCTATTGT 59.930 43.478 0.00 0.00 0.00 2.71
248 261 3.432252 GTCCGACCACTTTGTGTCTATTG 59.568 47.826 0.00 0.00 0.00 1.90
249 262 3.556423 GGTCCGACCACTTTGTGTCTATT 60.556 47.826 13.05 0.00 38.42 1.73
250 263 2.028385 GGTCCGACCACTTTGTGTCTAT 60.028 50.000 13.05 0.00 38.42 1.98
251 264 1.342174 GGTCCGACCACTTTGTGTCTA 59.658 52.381 13.05 0.00 38.42 2.59
252 265 0.106149 GGTCCGACCACTTTGTGTCT 59.894 55.000 13.05 0.00 38.42 3.41
253 266 0.883370 GGGTCCGACCACTTTGTGTC 60.883 60.000 19.43 0.00 41.02 3.67
254 267 1.147600 GGGTCCGACCACTTTGTGT 59.852 57.895 19.43 0.00 41.02 3.72
255 268 0.179029 AAGGGTCCGACCACTTTGTG 60.179 55.000 19.43 0.00 41.02 3.33
256 269 0.108019 GAAGGGTCCGACCACTTTGT 59.892 55.000 19.43 0.00 41.02 2.83
257 270 0.605589 GGAAGGGTCCGACCACTTTG 60.606 60.000 19.43 0.00 41.02 2.77
258 271 1.759236 GGAAGGGTCCGACCACTTT 59.241 57.895 19.43 9.96 41.02 2.66
259 272 2.222013 GGGAAGGGTCCGACCACTT 61.222 63.158 19.43 17.88 46.04 3.16
260 273 2.606826 GGGAAGGGTCCGACCACT 60.607 66.667 19.43 10.80 46.04 4.00
261 274 3.714001 GGGGAAGGGTCCGACCAC 61.714 72.222 19.43 8.70 46.04 4.16
268 281 4.735599 AGGGTCCGGGGAAGGGTC 62.736 72.222 0.00 0.00 0.00 4.46
296 309 2.897350 GCCGGGTGCATGTAGCTC 60.897 66.667 12.77 2.62 45.94 4.09
297 310 3.402681 AGCCGGGTGCATGTAGCT 61.403 61.111 4.72 1.17 45.94 3.32
298 311 3.204827 CAGCCGGGTGCATGTAGC 61.205 66.667 22.48 4.21 44.83 3.58
299 312 3.204827 GCAGCCGGGTGCATGTAG 61.205 66.667 44.63 16.66 43.41 2.74
306 319 0.970427 AATAAAAGGGCAGCCGGGTG 60.970 55.000 29.14 29.14 0.00 4.61
307 320 0.970427 CAATAAAAGGGCAGCCGGGT 60.970 55.000 5.00 0.00 0.00 5.28
308 321 0.682855 TCAATAAAAGGGCAGCCGGG 60.683 55.000 5.00 0.00 0.00 5.73
309 322 1.067516 CATCAATAAAAGGGCAGCCGG 59.932 52.381 5.00 0.00 0.00 6.13
310 323 1.750778 ACATCAATAAAAGGGCAGCCG 59.249 47.619 5.00 0.00 0.00 5.52
311 324 6.209391 ACATATACATCAATAAAAGGGCAGCC 59.791 38.462 1.26 1.26 0.00 4.85
312 325 7.219484 ACATATACATCAATAAAAGGGCAGC 57.781 36.000 0.00 0.00 0.00 5.25
314 327 8.739039 GCATACATATACATCAATAAAAGGGCA 58.261 33.333 0.00 0.00 0.00 5.36
315 328 7.910162 CGCATACATATACATCAATAAAAGGGC 59.090 37.037 0.00 0.00 0.00 5.19
316 329 7.910162 GCGCATACATATACATCAATAAAAGGG 59.090 37.037 0.30 0.00 0.00 3.95
317 330 7.910162 GGCGCATACATATACATCAATAAAAGG 59.090 37.037 10.83 0.00 0.00 3.11
318 331 8.668353 AGGCGCATACATATACATCAATAAAAG 58.332 33.333 10.83 0.00 0.00 2.27
319 332 8.450180 CAGGCGCATACATATACATCAATAAAA 58.550 33.333 10.83 0.00 0.00 1.52
320 333 7.821846 TCAGGCGCATACATATACATCAATAAA 59.178 33.333 10.83 0.00 0.00 1.40
321 334 7.327214 TCAGGCGCATACATATACATCAATAA 58.673 34.615 10.83 0.00 0.00 1.40
322 335 6.872920 TCAGGCGCATACATATACATCAATA 58.127 36.000 10.83 0.00 0.00 1.90
327 340 5.982356 AGATTCAGGCGCATACATATACAT 58.018 37.500 10.83 0.00 0.00 2.29
331 344 4.541973 TGAGATTCAGGCGCATACATAT 57.458 40.909 10.83 0.00 0.00 1.78
333 346 2.874701 GTTGAGATTCAGGCGCATACAT 59.125 45.455 10.83 0.00 0.00 2.29
363 376 4.576053 GGTGCACAGATTAAGCATCACATA 59.424 41.667 20.43 0.00 40.78 2.29
441 459 1.610624 CCACAGCCTGTAAACGGTGAT 60.611 52.381 0.00 0.00 34.43 3.06
442 460 0.250124 CCACAGCCTGTAAACGGTGA 60.250 55.000 0.00 0.00 34.43 4.02
443 461 0.534203 ACCACAGCCTGTAAACGGTG 60.534 55.000 3.94 0.00 0.00 4.94
444 462 0.534203 CACCACAGCCTGTAAACGGT 60.534 55.000 0.00 0.00 0.00 4.83
445 463 0.250124 TCACCACAGCCTGTAAACGG 60.250 55.000 0.00 0.00 0.00 4.44
454 472 1.360192 GTTGTGCTTCACCACAGCC 59.640 57.895 0.00 0.00 45.51 4.85
470 488 1.481772 AGCACAACCAGCACAAATGTT 59.518 42.857 0.00 0.00 0.00 2.71
472 490 2.228138 AAGCACAACCAGCACAAATG 57.772 45.000 0.00 0.00 0.00 2.32
484 502 9.595823 GTTCACCTATCTACTATTAAAGCACAA 57.404 33.333 0.00 0.00 0.00 3.33
516 538 1.157870 ACAAAGTTCAGTCCGCGGTG 61.158 55.000 27.15 17.74 0.00 4.94
569 591 3.744660 TCTTTGAAGGAAGAAGAGCACC 58.255 45.455 0.00 0.00 32.95 5.01
581 603 3.254903 CCGTTAGGGGTTTTCTTTGAAGG 59.745 47.826 0.00 0.00 0.00 3.46
594 616 1.219935 CCGAGGAAACCGTTAGGGG 59.780 63.158 0.00 0.00 43.47 4.79
595 617 0.108472 GTCCGAGGAAACCGTTAGGG 60.108 60.000 0.00 0.00 43.47 3.53
598 620 0.318120 GTGGTCCGAGGAAACCGTTA 59.682 55.000 0.00 0.00 38.45 3.18
640 663 6.183360 GCTTTTGGCTCAAAGATATCTCCAAT 60.183 38.462 18.57 0.00 34.72 3.16
858 881 1.621992 AGGACACGAGACAGTGACAT 58.378 50.000 0.00 0.00 44.43 3.06
996 1019 1.618343 GGGTAAGTTGCTGCCATTGTT 59.382 47.619 0.00 0.00 0.00 2.83
1011 1034 2.054799 GGTGGATCAGGCATAGGGTAA 58.945 52.381 0.00 0.00 0.00 2.85
1188 1211 1.005630 GTCGCTTGTGAGGCTCAGT 60.006 57.895 19.38 0.00 0.00 3.41
1464 1487 1.152756 GGACAGGTGCACAAACCCT 60.153 57.895 20.43 2.53 41.54 4.34
1670 1693 0.673022 CTCAGCCTTCACTGCACTCC 60.673 60.000 0.00 0.00 37.59 3.85
1708 1732 0.622136 ACCAGGCTCATCTGCATCAA 59.378 50.000 0.00 0.00 33.64 2.57
1790 1814 2.040606 GGGGAGGAGCCTGTGGTA 59.959 66.667 0.00 0.00 36.66 3.25
1924 1948 1.141881 GGCGCCTCAGAAGAATCGA 59.858 57.895 22.15 0.00 0.00 3.59
2100 2124 2.308690 GTTATCAGCCGAGGGACTACT 58.691 52.381 0.00 0.00 41.55 2.57
2121 2145 2.735663 TCTCTGTTGTACTCGAGTCGAC 59.264 50.000 23.89 21.32 0.00 4.20
2195 2219 1.470494 GCAGCAACTTAGAAGAAGGCC 59.530 52.381 0.00 0.00 0.00 5.19
2242 2269 3.070018 CCTTAGTGAGGCAAACAGAGTG 58.930 50.000 0.00 0.00 39.09 3.51
2361 2389 6.617879 TGCAGTAGTACACTATGTTACACAG 58.382 40.000 2.52 0.00 34.98 3.66
2391 2475 9.624373 AAATGTAGAAGCAGATCATGAAGTAAT 57.376 29.630 0.00 0.00 0.00 1.89
2393 2477 8.260114 TCAAATGTAGAAGCAGATCATGAAGTA 58.740 33.333 0.00 0.00 0.00 2.24
2398 2482 6.922247 ACTCAAATGTAGAAGCAGATCATG 57.078 37.500 0.00 0.00 0.00 3.07
2438 2524 5.457140 TGAACGAATTTCACACATTAAGCC 58.543 37.500 0.00 0.00 39.45 4.35
2466 2556 7.168219 TGTGTTAGCTGATGTAAATCCTTCTT 58.832 34.615 0.00 0.00 0.00 2.52
2486 2576 4.422073 TGACAGAGTTTCCTGATGTGTT 57.578 40.909 0.00 0.00 37.59 3.32
2502 2592 9.447040 CAAGAGAATATATTGTGCAAATGACAG 57.553 33.333 1.78 0.00 0.00 3.51
2520 2612 6.992063 ATAATTTGTGCGACTCAAGAGAAT 57.008 33.333 3.73 0.00 0.00 2.40
2521 2613 6.801539 AATAATTTGTGCGACTCAAGAGAA 57.198 33.333 3.73 0.00 0.00 2.87
2532 2624 7.015226 TCTGTGGATCTTAATAATTTGTGCG 57.985 36.000 0.00 0.00 0.00 5.34
2562 2660 4.288626 ACCACCTTTCTCCTGTAATTAGCA 59.711 41.667 0.00 0.00 0.00 3.49
2563 2661 4.844884 ACCACCTTTCTCCTGTAATTAGC 58.155 43.478 0.00 0.00 0.00 3.09
2565 2663 7.563724 AGTTACCACCTTTCTCCTGTAATTA 57.436 36.000 0.00 0.00 0.00 1.40
2606 2704 2.452600 TTCCTGCCCTGTTTCTTTGT 57.547 45.000 0.00 0.00 0.00 2.83
2631 2730 7.555554 GCTTCCTGACATATATTTGCCATCTAT 59.444 37.037 0.00 0.00 0.00 1.98
2837 2939 4.537688 TGAAATCACTGAATTCTCCCCTCT 59.462 41.667 7.05 0.00 0.00 3.69
2961 3080 1.044611 ATAAGGAGAAGGAGAGCGCC 58.955 55.000 2.29 0.00 0.00 6.53


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.